I have the service manual for my car as a bunch of hyperlinked PDFs; ie., there's a main index pdf, with hyperlinks to each section, each of which resides in a sub-folder. Each section then has an index pdf, and an actual contents pdf (or several)

I'm guessing this won't be supported, and transfer via Calibre will probably mess with the folders? I don't want to just "try and see", as there are around 100 files, and things could get messy trying to remove them again.

Any thoughts? I guess I could just make copies and rename each pdf to something meaningful, but it's a bit of a pain when sections say to refer to section x, with a hyperlink, then trying to track down where that bit is.

I don't know if the Kobo devices support hyperlinked PDF. I would expect not. But, if you have a file/directory structure on you PC that works, copy that to the device. Don't use calibre as it will want to rename the files.